VMD-L Mailing List

From: dhacademic (dhacademic_at_gmail.com)
Date: Thu Jan 13 2011 - 13:08:17 CST

Many thanks for the reply. It does work now.

I have another question about using variable in TCL. There are 34 subunits
(resid 1~34) in my system. I want to print out all of the intra-subunit
vectors of two atoms (atom name C3 and C17) in each frame. Results in the
outfile are printed out in a matrix, in which the ith column is the vector
of ith subunit and the jth line is the vector of jth frame. Following is the
loop part of my script, but it does not work. Can anyone help me to figure
out this problem?

Thanks in advance!

Best,
Hao

        for {set frame 0} {$frame < $num_steps} {incr frame} {
                set mynum 34
                for {set myid 1} {$myid < $mynum} {incr $myid} {
                        set s$myid [[atomselect $mol "resname CLT and name
C3 and resid $myid" frame $frame] get {x y z}]
                        set t$myid [[atomselect $mol "resname CLT and name
C17 and resid $myid" frame $frame] get {x y z}]
                        set vec$myid [vecsub ${s$myid} ${t$myid}]
                }
                puts $outfile "$vec1, $vec2, ...."

        }

On Thu, Jan 13, 2011 at 10:53 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> When you run a script like that, you need to make sure you add "waitfor
> all"
> to the end of the "mol new" and "mol addfile" commands, otherwise VMD
> continues running the next commands in your script while it is still
> in the process of loading the trajectory file in the background...
> So, this is why only 8 frames are loaded when you run it without the
> "waitfor all" option.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jan 13, 2011 at 10:45:16AM -0500, dhacademic wrote:
> > Hi VMD user,
> >
> > I meet the problem in extracting the number of frames from amber
> > trajectory.
> >
> > Following is my script "myframe.tcl". When I run "vmd -e myframe.tcl",
> the
> > calculated frame number is 8. But when I use the first two lines of
> the
> > script to load the trajectory, and then type in the last four lines in
> TCL
> > Console, the frame number is 1000. In reality, 1000 is the correct
> number.
> >
> > I want to know is there anything wrong?
> >
> > Best,
> > Hao
> >
> >
> > mol new out.top type parm7
> > mol addfile out.mdcrd type crdbox
> >
> > proc myframe {{mol top}} {
> > set num_steps [molinfo $mol get numframes]
> > }
> > myframe
> >
> >
> > 2011-01-13
> >
> > ----------------------------------------------------------------------
> >
> > dhacademic
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>